Package ontologyIndex

February 6, 2017
Type Package
Title Functions for Reading Ontologies into R
Version 2.4
Date 2017-02-01
Author Daniel Greene <dg333@cam.ac.uk>
Maintainer Daniel Greene <dg333@cam.ac.uk>
Description Functions for reading ontologies into R as lists and manipulating sets of ontologi-
cal terms - 'ontologyX: A suite of R packages for working with ontologi-
cal data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.
License GPL (>= 2)
Depends R (>= 3.1.0)
Suggests knitr, ontologySimilarity, ontologyPlot
VignetteBuilder knitr
RoxygenNote 5.0.1
NeedsCompilation no
Repository CRAN
Date/Publication 2017-02-06 14:21:31

R topics documented:
ontologyIndex-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
exclude_descendants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
get_ancestors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
get_descendants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
get_ontology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
get_relation_names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
get_term_descendancy_matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
get_term_frequencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
get_term_info_content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
get_term_property . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1
2 ontologyIndex-package

go . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
hpo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
intersection_with_descendants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
minimal_set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
mpo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
ontology_index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
print.ontology_index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
propagate_relations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
prune_descendants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Index 14

ontologyIndex-package Functions for Reading Ontologies into R

Description
Functions for reading ontologies into R and manipulating sets of ontological terms.

Details

Package: ontologyIndex
Type: Package
Version: 2.0
Date: 2016-07-20
License: GPL (>= 2)

The key functions include get_ontology for creating the index, get_ancestors for computing
the set of all terms which are ancestors of at least one from set of terms and get_descendants for
getting all terms which descend from a term. The package comes with R objects hpo, mpo and go
which index the Human Phenotype Ontology, Mammalian Phenotype Ontology and Gene Ontology
respectively.

Author(s)
Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>

References
Westbury SK, Turro E, Greene D, Lentaigne C, Kelly AM, Bariana TK, Simeoni I, Pillois X,
Attwood A, Austin S, Jansen SB, Bakchoul T, Crisp-Hihn A, Erber WN, Favier R, Foad N, Gat-
tens M, Jolley JD, Liesner R, Meacham S, Millar CM, Nurden AT, Peerlinck K, Perry DJ, Poudel P,
Schulman S, Schulze H, Stephens JC, Furie B, Robinson PN, Geet Cv, Rendon A, Gomez K, Laffan
MA, Lambert MP, Nurden P, Ouwehand WH, Richardson S, Mumford AD and Freson K (2015).
check 3

Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases
with unexplained bleeding and platelet disorders. _Genome Med_, *7*(1), pp. 36.
Kohler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL,
Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst
JA, Jahn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A,
Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO,
Wright CF, Vulto-van Silfhout A, de Leeuw N, de Vries B, Washingthon NL, Smith CL, Wester-
field M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE and Robinson PN
(2014). The Human Phenotype Ontology project: linking molecular biology and disease through
phenotype data. _Nucleic Acids Res._, *42*(Database issue), pp. D966-974.
Ashburner et al. Gene ontology: tool for the unification of biology (2000) Nat Genet 25(1):25-9
Smith, Cynthia L., Carroll-Ann W. Goldsmith, and Janan T. Eppig. The Mammalian Phenotype
Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome
biology 6.1 (2004): 1.

check Perform simple consistency checks on ontology_index object

Description
Perform simple consistency checks on ontology_index object

Usage
check(ontology, stop_if_invalid = FALSE)

Arguments
ontology ontology_index object.
stop_if_invalid
Logical value determining whether the function should call stop and print an
error message upon finding that the given ontology_index is in valid.

exclude_descendants Exclude terms descending from any in a given set of root terms

Description
Exclude from set terms, any terms that are either in, or descend from one of, the set roots.

Usage
exclude_descendants(ontology, roots, terms)
4 get_ancestors

Arguments
ontology ontology_index object.
roots Character vector of IDs for terms with respect to which descendants are to be
defined.
terms Character vector of ontological terms.

Value
Character vector of terms

See Also
intersection_with_descendants, prune_descendants

get_ancestors Get set of terms containing all ancestors of terms in a given set

Description
Get set of terms containing all ancestors of terms in a given set

Usage
get_ancestors(ontology, terms)

Arguments
ontology ontology_index object.
terms Character vector of ontological terms.

Value
Character vector of all terms which are an ancestor of at least one term in terms, including the
terms themselves

See Also
link{get_descendants}

Examples
data(hpo)
get_ancestors(hpo, c("HP:0001873", "HP:0011877"))
get_descendants 5

get_descendants Get set of terms containing all descendants of terms in a given set

Description
Get set of terms containing all descendants of terms in a given set

Usage
get_descendants(ontology, roots, exclude_roots = FALSE)

Arguments
ontology ontology_index object.
roots Character vector of IDs for terms with respect to which descendants are to be
defined.
exclude_roots Boolean determining whether to remove the given roots terms from the result.

Value
Character vector of terms

See Also
link{get_ancestors}

Examples
data(hpo)
get_descendants(hpo, roots="HP:0001873")

get_ontology Read ontology from OBO file into R

Description
Read ontology from OBO file into R

Usage
get_ontology(file, propagate_relationships = "is_a",
extract_tags = "minimal")

get_OBO(file, propagate_relationships = "is_a", extract_tags = "minimal")

6 get_relation_names

Arguments

file File path of OBO formatted file.

propagate_relationships
Character vector of relations
extract_tags Character value: either "minimal" or "everything", determining whether to ex-
tract only the properties of terms which are required to run functions in the
package - i.e. "id", "name", "parents", "children" and "ancestors" -
or extract all properties provided in the file. Defaults to "minimal".

Value

ontology_index object.

See Also

get_relation_names

get_relation_names Get names of relations used in OBO file

Description

Get names of relations used in OBO file

Usage

get_relation_names(file)

Arguments

file File path of OBO formatted file.

See Also

get_ontology
get_term_descendancy_matrix 7

get_term_descendancy_matrix
Get logical descendancy matrix for set of terms

Description
Get logical descendancy matrix for set of terms

Usage
get_term_descendancy_matrix(ontology, terms = NULL, rows = terms,
cols = terms)

Arguments
ontology ontology_index object.
terms Character vector of ontological terms.
rows Rows for resultant matrix (defaults to terms).
cols Cols for resultant matrix (defaults to terms).

Value
A logical square matrix of with length(terms) columns and rows. result[row_term,col_term] == TRUE
if row_term is an ancestor (and not the same as) of col_term.
A logical matrix.

Examples
data(hpo)
get_term_descendancy_matrix(hpo, c("HP:0001873", "HP:0011877"))

get_term_frequencies Get frequency of each term in a set of phenotypes

Description
Get frequency of each term in a set of phenotypes

Usage
get_term_frequencies(ontology, term_sets, patch_missing = FALSE)
8 get_term_info_content

Arguments
ontology ontology_index object.
term_sets List of character vectors of ontological term IDs.
patch_missing Logical indicating whether to include whole ontology even if theyre not present
in the term_sets as if they had occurred once

Value
Numeric vector of information contents, named by corresponding terms. Takes into account ances-
tors, in the sense that all ancestor terms implied by the phenotypes are considered on

See Also
get_term_info_content

Examples
data(hpo)
get_term_frequencies(hpo, list("HP:0001873"))

get_term_info_content Get information content of each term in a set of phenotypes

Description
Get information content of each term in a set of phenotypes

Usage
get_term_info_content(ontology, term_sets, patch_missing = FALSE)

Arguments
ontology ontology_index object.
term_sets List of character vectors of ontological term IDs.
patch_missing Logical indicating whether to include all ontology terms even if theyre not
present in the term_sets as if they had occurred once

Value
Numeric vector of information contents, named by corresponding terms. Takes into account ances-
tors, in the sense that all ancestor terms implied by the phenotypes are considered on

Examples
data(hpo)
get_term_info_content(hpo, list("HP:0001873"))
get_term_property 9

get_term_property Get property of individual ontological term

Description
Get property of individual ontological term

Usage
get_term_property(ontology, property_name, term, as_names = FALSE)

Arguments
ontology ontology_index object.
property_name Name of property.
term Character value of term ID.
as_names Logical value determining whether to return character vector of names (defaults
to FALSE).

go GO index

Description
ontology_index object encapsulating structure of the Gene Ontology (HPO) comprising a list of
lists/vectors of properties of GO terms indexed by term ID

Format
List of lists and vectors

hpo HPO index

Description
ontology_index object encapsulating structure of the Human Phenotype Ontology (HPO) com-
prising a list of lists/vectors of properties of HPO terms indexed by term ID

Format
List of lists and vectors
10 minimal_set

intersection_with_descendants
Intersect a set of terms with the descendants of a given set of roots

Description
Intersect a set of terms with the descendants of a given set of roots

Usage
intersection_with_descendants(ontology, roots, terms)

Arguments
ontology ontology_index object.
roots Character vector of IDs for terms with respect to which descendants are to be
defined.
terms Character vector of ontological terms.

Value
Character vector of terms

See Also
exclude_descendants, prune_descendants

Examples
data(hpo)
intersection_with_descendants(hpo, c("HP:0001872", "HP:0000707"), c("HP:0001873", "HP:0011877"))

minimal_set Remove redundant/implied terms from a set of terms

Description
Remove redundant/implied terms from a set of terms

Usage
minimal_set(ontology, terms)
mpo 11

Arguments
ontology ontology_index object.
terms Character vector of ontological terms.

Value
Character vector of terms

Examples
data(hpo)
minimal_set(hpo, c("HP:0001873", "HP:0001872"))

mpo MPO index

Description
ontology_index object encapsulating structure of the Mammalian Phenotype Ontology (MPO)
comprising a list of lists/vectors of properties of MPO terms indexed by term ID

Format
List of lists and vectors

ontology_index Create ontology_index object from vectors and lists of term proper-
ties

Description
Create ontology_index object from vectors and lists of term properties

Usage
ontology_index(parents, id = names(parents), name = id,
obsolete = setNames(nm = id, rep(FALSE, length(id))), version = NULL, ...)

Arguments
parents List of character vectors of parents per term.
id Character vector of term IDs. Defaults to the "names" attribute of the parents
argument and must be the same length as parents.
name Character vector of term labels.
obsolete Logical vector indicating whether given terms are obsolete.
version Version information about the ontology.
... Additional arguments, each of which should be either a vector or list of term
properties, each with the same length as id.
12 propagate_relations

Examples
animal_superclasses <- list(animal=character(0), mammal="animal", cat="mammal", fish="animal")
animal_ontology <- ontology_index(parents=animal_superclasses)
unclass(animal_ontology)

print.ontology_index Print ontology_index object.

Description
Print ontology_index object.

Usage
## S3 method for class 'ontology_index'
print(x, ...)

Arguments
x ontology_index object.
... Unused parameters.

Value
Prints a summary

propagate_relations Select terms by propagating relations from a set of terms

Description
An ontology_index can contain multiple relations (for example in the case of the Gene Ontology,
"is_a" and "part_of" could be stored as separate properties in an ontology_index). Transitive
relations (i.e. relations such that x related to y and y related to z implies x related to z, for example
the relation is an ancestor of) stored by an ontology_index can be propagated using this function.
The inverse relations (i.e. x inversely related to y if y related to x) can also be propagated by setting
the use_inverse_relations parameter to TRUE.

Usage
propagate_relations(ontology, roots, relations, use_inverse_relations = FALSE,
exclude_roots = FALSE)
prune_descendants 13

Arguments
ontology ontology_index object.
roots Character vector of term IDs from which relations will be propagated.
relations Character vector given names of transitive relations to be propagated.
use_inverse_relations
Boolean vector indicating whether to propagate inverse relations. If use_inverse_relations
is the same length as relations, each element determines whether the corre-
sponding relation in relations is inverted.
exclude_roots Boolean determining whether to remove the given roots terms from the result.

Value
Character vector of terms

See Also
get_ancestors, get_descendants

prune_descendants Exclude terms descending from a given set of roots but include those
roots which were originally implicitly present.

Description
Given two sets of terms, roots and terms, construct a set of terms containing those in terms which
do not descend from any term in roots, and also any terms in roots which are ancestors of any
term in terms.

Usage
prune_descendants(ontology, roots, terms)

Arguments
ontology ontology_index object.
roots Character vector of IDs for terms with respect to which descendants are to be
defined.
terms Character vector of ontological terms.

Value
Character vector of terms

See Also
exclude_descendants, intersection_with_descendants
Index

check, 3

exclude_descendants, 3, 10, 13

get_ancestors, 2, 4, 13
get_descendants, 2, 5, 13
get_OBO (get_ontology), 5
get_ontology, 2, 5, 6
get_relation_names, 6, 6
get_term_descendancy_matrix, 7
get_term_frequencies, 7
get_term_info_content, 8, 8
get_term_property, 9
go, 9

hpo, 9

intersection_with_descendants, 4, 10, 13

minimal_set, 10
mpo, 11

ontology_index, 11
ontologyIndex (ontologyIndex-package), 2
ontologyIndex-package, 2

print.ontology_index, 12
propagate_relations, 12
prune_descendants, 4, 10, 13

14